goldMINER 2.0.27 – Use CDD to Automate Sequence Annotation

goldMINER 2.0.27

:: DESCRIPTION

goldMINER automates local and remote searches against pFAM and CDD (Conserved-Domain Database, which integrates pFAM, SMART and COG, etc.) databases searches to annotate sequences such as expressed sequence tags (ESTs). It is the first software package to use the power of CDD at NCBI to automate sequence annotation.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

goldMINER

:: MORE INFORMATION

N/A

SPICE 0.9 – Protein Sequences, Structures & Annotations Browser

SPICE 0.9

:: DESCRIPTION

SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

::DEVELOPER

Andreas Prlic, Thomas Down, Tim Hubbard.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

SPICE

:: MORE INFORMATION

Citation:

Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard

annot8r 1.1.1 – BLAST based GO-EC-KEGG Annotation

annot8r 1.1.1

:: DESCRIPTION

annot8r is a tool for the annotation of protein or nucleotide sequences from non model organisms with GO terms, EC numbers and KEGG pathways. The annotation is based on BLAST similarity searches against annotated subsets of EMBL UniProt from which sequences with non-informative entries have been removed. GO, EC and KEGG annotations are saved as flat files and in a relational postgreSQL database to allow for more sophisticated searches within the results.

::DEVELOPER

Ralf Schmid and Mark Blaxter

:: REQUIREMENTS

:: DOWNLOAD

annot8r

:: MORE INFORMATION

DIYA 1.0.1 – Microbial Genome Sequences Annotation

DIYA 1.0.1

:: DESCRIPTION

DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline framework, written in Perl, used for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence.

::DEVELOPER

Navy Medical Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Perl

:: DOWNLOAD

DIYA

:: MORE INFORMATION

Citation:

Andrew C. Stewart, Brian Osborne and Timothy D. Read
DIYA: a bacterial annotation pipeline for any genomics lab
Bioinformatics (2009) 25 (7): 962-963.doi: 10.1093

mVISTA – Compare Sequences & Visualize Alignments with Annotation Information

mVISTA

:: DESCRIPTION

mVISTA is a set of programs for comparing DNA sequences from two or more species up to megabases long and visualize these alignments with annotation information. mVISTA has a clean output, allowing for easy identification of sequence similarities and differences, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is implemented as an on-line server that provides access to global pairwise, multiple and glocal (global with rearrangements) alignment tools.

mVISTA web version

::DEVELOPER

Genomics Division of Lawrence Berkeley National Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • JAVA

:: DOWNLOAD

mVISTA

:: MORE INFORMATION

mVISTA and Avid are free for academic or non-profit research institutions to use for internal research purposes. Commercial companies may submit sequences over the Web using the VISTA web site at no charge. To obtain a copy of mVISTA or Avid for internal use, commercial entities are required to purchase a site license for commercial use.

Citation:

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9

Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence Alignments of Arbitrary Length. Bioinformatics, 16:1046.